I used the lower one on the front of the engine. The DPF on my 3725 is larger than the muffer you have and makes access to the filler in the valve cover more difficult.
Somewhere on this forum I read about someone who filled the engine from the valve cover and the oil didn't drain down into the crankcase before the engine was started, and it was damaged. I don't know if that was the real problem. I could see on some engines that the oil drain from the top end might not be very large, especially if the engine does not pump a lot of oil up there. Modern car/truck engines circulate a lot of oil and have good drainage from the top end so this shouldn't be a problem for them. In any case, checking the dipstick before starting would ensure that there's oil in the sump.
BTW my 3725's dipstick is really long and has multiple hash marks on it, like five or six of them. I filled it the amount that the manual calls for and it goes to the top mark. That's where the level was when the tractor was delivered. Yours might be different,.